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Structure paper

TitleStructural insights into chromatin remodeling by ISWI during active ATP hydrolysis.
Journal, issue, pagesScience, Vol. 388, Issue 6751, Page eadu5654, Year 2025
Publish dateJun 5, 2025
AuthorsYouyang Sia / Han Pan / Kangjing Chen / Zhucheng Chen /
PubMed AbstractChromatin remodelers utilize the energy of adenosine triphosphate (ATP) hydrolysis to slide nucleosomes, regulating chromatin structure and gene activity in cells. In this work, we report structures ...Chromatin remodelers utilize the energy of adenosine triphosphate (ATP) hydrolysis to slide nucleosomes, regulating chromatin structure and gene activity in cells. In this work, we report structures of imitation switch (ISWI) bound to the nucleosome during active ATP hydrolysis and remodeling, revealing conformational transitions of the remodeling motor across the adenosine triphosphatase (ATPase) cycle. The DNA strands were distorted accordingly, showing one full base-pair bulge and a loss of histone contact at the site of motor binding in the adenosine diphosphate* (ADP*) and apo* (unbound) states. We also identified several important elements for regulation of the remodeling activity. Notably, an enzyme conformation exiting the remodeling cycle reveals a linker DNA-sensing brake mechanism. Together, our findings elucidate a multistate model of ISWI action, providing a comprehensive mechanism of DNA translocation and regulation underpinning chromatin remodeling.
External linksScience / PubMed:40179160
MethodsEM (single particle)
Resolution2.3 - 3.3 Å
Structure data

61624

9jnp

EMDB-61624, PDB-9jnp:
Structure of isw1-nucleosome complex in ATP state
Method: EM (single particle) / Resolution: 2.3 Å

61626

9jnt

EMDB-61626, PDB-9jnt:
Structure of isw1-nucleosome complex in ADP* state
Method: EM (single particle) / Resolution: 2.7 Å

61627

9jnu

EMDB-61627, PDB-9jnu:
Structure of isw1-nucleosome complex in ADP state
Method: EM (single particle) / Resolution: 2.5 Å

61628

9jnv

EMDB-61628, PDB-9jnv:
Structure of isw1-nucleosome complex in ADP(S) state
Method: EM (single particle) / Resolution: 3.0 Å

61629

9jnw

EMDB-61629, PDB-9jnw:
Structure of isw1-nucleosome complex in ADP+ state
Method: EM (single particle) / Resolution: 2.9 Å

61630

9jnx

EMDB-61630, PDB-9jnx:
Structure of isw1-nucleosome complex in ADP*+ state
Method: EM (single particle) / Resolution: 3.0 Å

61632

9jnz

EMDB-61632, PDB-9jnz:
Structure of isw1-nucleosome complex in Apo state
Method: EM (single particle) / Resolution: 3.0 Å

61641

9jo2

EMDB-61641, PDB-9jo2:
Structure of isw1-nucleosome complex in Apo* state
Method: EM (single particle) / Resolution: 3.0 Å

61644

9jo5

EMDB-61644, PDB-9jo5:
Structure of isw1-nucleosome complex in ADP-B state
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-61647: structure of nucleosome in ATP state
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-61649: structure of nucleosome in ADP state
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-61650: structure of nucleosome in ADP* state
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-61651: Structure of nucleosome in ADP-S state
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-61652: structure of nucleosome in ADP+ state
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-61653: structure of nucleosome in ADP*+ state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-61654: structure of nucleosome in Apo state
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-61655: structure of nucleosome in Apo* state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-61657: structure of isw1-motor in ATP state
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-61658: structure of isw1-motor in ADP state
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-61660: Structure of isw1-motor in ADP-S state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-61661: structure of isw1-motor in ADP* state
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-61662: structure of isw1-motor in ADP+ state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-61663: structure of isw1-motor in ADP*+ state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-61665: strcuture of isw1-motor in Apo state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-61667: structure of isw1-motor in Apo* state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-61669: Structure of isw1-motor in ADP-B state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-61671: Structure of isw1-lobe2 in ADP-B state
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-61672: Structure of nucleosome in ADP-B state
Method: EM (single particle) / Resolution: 2.7 Å

63123

9liu

EMDB-63123, PDB-9liu:
Structure of isw1-nucleosome double-bound complex in ATP-ATP state
Method: EM (single particle) / Resolution: 2.7 Å

63131

9lj2

EMDB-63131, PDB-9lj2:
Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state
Method: EM (single particle) / Resolution: 2.98 Å

EMDB-63134: Structure motor1 of isw1-nucleosome double-bound complex in ATP-ATP state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-63135: Structure of motor2 of isw1-nucleosome double-bound complex in ATP-ATP state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-63136: Structure of nucleosome of isw1-nucleosome double-bound complex in ATP-ATP state
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-63138: Structure of motor1 of isw1-nucleosome double-bound complex in ADP-ADP+ state
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-63139: Structure of motor2 of isw1-nucleosome double-bound complex in ADP-ADP+ state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-63143: Structure of nucleosome of isw1-nucleosome double-bound complex in ADP-ADP+ state
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-CL:
Unknown entry

Source
  • Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
  • xenopus laevis (African clawed frog)
  • saccharomyces cerevisiae s288c (yeast)
  • escherichia coli k-12 (bacteria)
  • Saccharomyces cerevisiae (brewer's yeast)
KeywordsDNA BINDING PROTEIN/DNA / Chromatin Remodeler / Nucleosome / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN

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